Category Archives: Data Review

TF 3.0 Export Results Grid to Excel and Copy Images to Clip Board

Sticking to new features in data review, we’ll continue with a simple workflow.

One of the many request that TraceFinder has received over the last year has been to have the ability to export the results grid directly to Excel instead of having a Custom Report generated.

In TF 3.0 all data grid results whether in the quantitative views or targeted screening section, export all data to Excel or CSV files directly.

No need to produce a custom report and navigate through the files menus to go get it.

Simply export and place the file where you want it.

Also a feature that has been requested is the ability to copy high definition images of chromatograms and such to the clipboard for use in papers, lab notebooks and presentations/posters.

We also did this in TF 3.0

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

 

New TF 3.0 Targeted Screening Workflow in Data Review (or the marriage of TF and ExactFinder)

A new feature to TraceFinder 3.0 is targeted screening. The workflow and method setup that were included in ExactFinder has been included in TraceFinder 3.0. Though it has been expanded to support Nominal Mass as well as HRAM.

That means this feature will work for all mass spectrometers from the GC single quads to the Q-Exactive.

Though some sections are more geared for HRAM, they can just not be used when using nominal mass data.

The other aspect is that TF gives you the ability to acquire, process and report on the fly during acquisition. Therefore, if you so choose you don’t have to wait to review your data. So this expands the capabilities that was introduced in ExactFinder.

This is our first step with this functionality and more is to come in following releases, but there are some interesting things that can be done by having these two workflows combined.

Again the video is a little longer that my 2 minute rule but there is a lot to look forward to.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

New TraceFinder 3.0 Data Review Elements

In TraceFinder 3.0, you will find that we have changed the Graphical User Interface quite a bit. Other than changing some of the colors and the navigation style we have also added elements to help review data in a way that can be tailored.

A concept that came across to our team was to help tell the story of the data. This is what TraceFinder was intended to do from its concept. We realized that many scientist that will use this and related products will not be “CLASSICAL” mass spec people. Young new chemist or other scientist not use to mass spec data moving into the lab need to be able to see what they need to know about the data and have a feel on what works best for them. At the end of the day they are telling the story of the data to their customers.

Our concept is to give you the ability to choose what you want to see and how you want to see it.

In forthcoming releases you will have the ability to “Read the Cliff Notes” of the data or the other end of the spectrum of reading “War and Peace,” if you so choose. We don’t want to limit the data or have the data be so overwhelming it can’t make sense.

So in this video we will show you how to navigate in the Compound and Sample Views which are just different ideas on how to look at the data. Also how to arrange the views so it makes sense, or makes it easier to read through the data.

A big plus is the ability to filter out data you don’t care to see or only data you are interested in.

All this and the views are remembered automatically when a User signs out or closes the application.

Although the video only takes place on one screen. Any part of the data review section is a dockable panel so you can have parts on multiple monitors and they will remain synced. I personally use a three monitor setup and have a multipeak panel on one, a detailed view on another and my data review grid on my main display.

Remember we can only make it better if we hear back from you so, please send in your ideas, comments or questions. The video is a little longer than my 2 minute rule but it should explain a lot of the NEW ELEMENTS and their functions.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

 

Associating another batch’s Calibration Curve to the current batch – (Answer to a “Ask A Guru” Question)

I think that the questions below are pretty self explanitory of the feature in the video.

What would you like to know?: Hi, Jamie,

 

Example: A Cal curve batch is acquiring. 

 

Case 1:  I submit a new batch of just patient samples and forget to extend the cal file to those samples.  How do I extend the cal file to those samples w/o pulling them into the Cal Curve batch?

 

Case 2:  I submit a new batch of just patient samples and  extend the cal (with the wrong file) to those samples.  How do I  reprocess with the correct cal file?

Company: TFS

Area Of work: Clinical”

So if you have a batch in flight. You should pause the acquisition while you associate a calibration file. It just makes things cleaner if you have an older system with less RAM.

The video is out of the soon to be released TF 3.0, but if you are using and older version the functionality and menu selections are still the same. Dependant on the resolution setting the last frame may be overlayed with another.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

Sneak Peek – Targeted Screening

As Always the TF team is looking forward and addressing market driven issues.

One thing that has become highly vocal in the applied markets is the ability to screen for target molecules, and then quantitatate on the positive hits.

So in a forth coming release, TF has incorporated the ExactFinder Screening workflow into its core set of capabilities.

We’ve expanded on this, to include nominal mass instruments, as well as, the high resolution accurate mass systems. This will allow for us to screen utilize screening from the single quandrupoles all the way to up to the QExactive.

So below is a shot of the new screening data review, and you can get an idea of the new UI style adopted by Thermo Scientific.

We still will have the same quan workflow, but have added acquistion and realtime reporting to ExactFinder screening workflow.

 

What the Heck is ACTIVE VIEW??????(Answer to a “Ask A Guru” question)

Active View is another visualization of the data that is on a Sample Centric Report. These are only availible today on samples that display chromatograms for compounds and contain grouped sample information.

Sucha as the High Density Reports, in the standard reports section of Report View.

When using Report View we generate a temporary view of the report that would be produced by the system. This view is only for the supplied Standard reports delivered with TF and is not available with Custom Reports, today. (Hint be looking to the future.)  😉

But when the report is generated in preview mode, and it has an ActiveView partner, the Active View tab will appear next to it.

In the Active View tab, you will see a grid of data that corresponds with data on the Report and the same Detailed Editing elements in Data Review, with the same functionality.

When data is changed in Active View it is just like editing in Data Review and results are updated.  When this happens and indicator appears to let you know new results are availible for the report. Once clisked the Report is updated. The information is saved. In this manner you can use Report View as your data editor and see exactly what you are giving your clients in real time. You can at this point choose to generate the report, or make all your edits and then generate the reports in a batch process.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

Matrix Spike and Matrix Spike Duplicate… Understanding the how it works.(Answer to a “Ask a Guru” question)

A question from the Ask a Guru was how to use MS/MSD samples and reports, well read below.

In the Environmental realm there is an experiment for a Matrix Spike and a duplicate, when compared to an unknown sample.

This allows for the chemist to calcualte a recovery of of the compounds contained in the unknown sample.

To set up the experiment the chemist needs three sample types.

  1. Matrix Spike – with compounds spiked into it at a known level
  2. Matrix Spike Duplicate –  with compounds spiked into it at the same level as the Matrix Spike
  3. Unknown – a sample with unknown amounts

Under QAQC tab of the Master/Local Method the concetrations of the spikes compounds must be entered in the grid for the MS and MSD tab.

In the Batch View the samples to be grouped together and used to report the Recovery must have the same SAMPLE ID. There must be one of each SAMPLE TYPE, but each one must have the sample SAMPLE  ID text in their individual grid cell.

When the batch is processed the data for recovery will be calcuated and a MS/MSD Report can be generated that displays the information about this experiment.

See the picture below of the report in Report View.

Thanks to Gail Harrison for her suggestion on a blog post.

Need To Look At Files With Data Dependant Experiments?

Though TraceFinder is primarily a quantitation application, it does have some provisions for unknown identification.

Mainly used in Single Quad or Ion Trap Analysis, the qualitative processing allows for scanning files along a TIC for peaks of interest and then eliminating the known targets and performing library searches against the unknown peaks. Also, TF gives the ability to look at the peaks that generate data dependant scans(DDS). It will sum the spectra and compare to a NIST style library.

To utilize this feature you must have two things. One a Method template, with the parameters set for Qualitative processing and DDS enabled, and a Sample Type of either and Unknown/TIC or Unknown Qual.

If you are performing Quantitative processing those will be perfromed first and Qualitative will occurs on the sample after Quan results are created.

If you have Qual resuts in data review you will have a green button to select the QualView.

Follow the the Video in setting up a Method Template and then using it in a Batch to review qualitative results.

If the video is blurry select the cog wheel in the lower right of the video window and adjust the resolution setting.

There Can Only Be One… Calibration Point

Even though its the most memorable line from the movie “Highlander”, this statement has come up many times for assays where semi quantitation occurs in screening analysis.

One way to accomplish a rough estimate calculated amount is to use the ability to use a single calibration level for a compound.

When you do this there are two settings in the Method setting that can be used.

Selecting Average RF allows for the average response factor for a calibration curve to be calcualted. If you use cal one point

the response of the point will be compared to the response of the compound in the sample and a rough estimate based on the

average will estimate the calcualted amount.

If using a linear curve and one point, you MUST set the Origin setting to Force. This sets the origin at Zero and draw the curve

the response of the one calibration point. Thereby giving you a curve to estimate the calcualted amount from.

There is a third way using Internal Standards, but we’ll save that for another day.

“Got Data?” – New Version on the way – TF 2.1

We are glad to announce that TraceFinder 2.1 is being cut to disks this week and will be on the shelves shortly.

The version has many “bug” fixes and performance improvements, but the BIGGEST feature is the ability to be run  on any detector Thermo supports. So if yo have a QExactive or a FID standalone GC, its supported. As well as, blended configurations.

So “Got Data?” we have a tool for you.

Plus soon to be published iBook for getting started with TF. “The Guru Guide”, written by the product manager for TraceFinder.

Remember if you have a question please fill out the form on the “Ask A Guru” tab. That message goes directly to the product manager or one of the support staff.